PG II Meeting Summary

PLANT GENOME RESEARCH BEGINS A NEW VOYAGE OF DISCOVERY
Brief Summary -- Plant Genome II Conference (San Diego, Calif.,
Jan. 24-27, 1994)
Susan McCarthy, USDA
National Agricultural Library, 4th Floor
10301 Baltimore Blvd.
Beltsville, MD 20705
February 24, 1994
Applications of genome mapping and analysis to solve existing
problems and uncover answers to fundamental questions relating to
the plant genome and its evolution were featured in the recent
Plant Genome II conference (San Diego, Calif., Jan 24-27, 1994).
The meeting attracted 553 participants from 22 countries.
According to Steven Oliver, University of Manchester, Manchester,
UK, we are entering a stage where the taxonomy of gene function
will be essential in efficiently identifying new genes. This new
age will require a multi-disciplinary approach encouraging the
collaboration of physiologists, geneticists, biochemists, and
plant breeders. He defined this era as a new voyage of the
Beagle.
The message was reinforced by Dr. James Cook, USDA, ARS and
Senior Scientist, CSRS, who pointed out that now is the time to
bring plant breeders together with molecular biologists to
conduct a gene hunt for agronomically important genes.
New insights
Understanding plant genome structure and organization can lead to
interesting and relevant discoveries as highlighted by Dr.
Richard Flavell, Director, John Innes Institute, Norwich, UK.
Understanding the role of epigenetic regulation, gene order, and
in situ homology sequence searching will ultimately help in the
practical application of biotechnology. Plants have had to
defend themselves from foreign DNA over the millennia and as a
result have developed strategies -- including gene silencing --
to cope with transposon selection pressures. The plant's ancient
art of anti-sense technology may take advantage of gene location.
Gene location would determine epigenetic DNA methylation events,
which in turn would regulate gene expression. In all, Flavell
points out, concerted evolution in the long term helps to
maintain high levels of conservation across the chromosome both
in terms of sequence and gene order or synteny.
Evidence of ancient transposon and retrotransposon events were
detected by Thomas Bureau, University of Georgia. Extensive
sequence similarity searches were performed on the GenBank and
EMBL nucleotide sequence databases. These "database mining"
experiments have identified over 100 normal plant gene sequences
showing evidence for a member of either the "Tourist" or
"Stowaway" family of transposons. The location of several
elements corresponds to previously reported cis-acting regulatory
elements. Significantly, a "Tourist" element was found to serve
as the promoter for the maize auxin-binding protein (abp1). The
first plant retrotransposon, Bs1, was found to contain a cellular
gene fragment: this provides the first evidence for transduction
by a retrotransposon in plants.
Progress in rice
The Japanese rice genome program reported significant advances.
A genetic map with 1400 RFLP and RAPD markers was described by
Dr. Nori Kurata, NIAR/STAFF, Japan. Over 7,500 clones from
callus tissue at different developmental stages have been
sequenced. Of those sequenced 1,800 are clones of known
function. Dr. Kurata reports that an expression map has been
constructed using cDNA mapping as a base. This map includes
information on tissue-specificity, distribution of isozyme genes,
gene families, and functionally related genes in the genome, such
as ribosomal protein genes and the histone gene family.
Physical mapping in the Japanese rice genome program will be used
to identify economically important genes. Two YAC and three
cosmid clone libraries have been developed, representing about
20% of the rice genome. Ordered libraries will be prepared from
these clone libraries. To date 120 YAC end-clones have been
isolated and end-clone mapping is underway. Typical YAC's have
400 kb inserts, which when finished the Japanese expect will
cover the rice genome 6 times over. Chromosomes 1, 4, 6, and 11
are being given high priority. It is known that a number of
important resistance genes reside on Chromosome 6. Mapping data
from the Japanese program have been entered onto two versions of
an internal database called RiceBase, one version contains mostly
cDNA information while the other version has the physical map
data.
International collaboration of rice mapping efforts was
encouraged by an informal workshop held in conjunction with the
conference, Dr. Susan McCouch, Cornell University, and Dr. Gou-
fan Hong, Director, Chinese Rice Genome Program co-chaired the
workshop. Dr. Kurata indicated that the Japanese mapping data
should be made public later this year. Five prime sequence data
for several hundred markers is currently available. Pamela
Ronald, University of California, Davis, CA, announced the
public availability of a variety of libraries including their
Bacterial Artificial Chromosomes and cosmids.
Physical mapping
Physical mapping was again highlighted in the Arabidopsis
workshop. Caroline Dean (John Innes Institute, Norwich, UK) and
Howard Goodman (Massachusetts General Hospital) reported that
chromosomes 4 and 5 are nearing completion in their joint effort
to integrate the two YAC and cosmid maps. A new YAC library
developed by David Bouchez should help in developing the
integrated physical map. Several thousand Arabidopsis cDNA's
have been sequenced by the French EST project. Michel Delseny,
(CNRS, Perpignon, France) reported on the project indicated that
the cDNA sequences have been deposited in the public database
Resources
Plant Genome II provided participants with information on useful
technologies and resources. The latest developments in the plant
genome databases were outlined, as well as computational tools
for mapping and sequence analysis. Database demonstrations with
a live Internet link were available throughout the meeting
allowing hands-on experience to interested researchers to test.
Electronic BIOSCI newsgroups were the focus of several workshops
organized by Dave Kristofferson, (Intelligenetics, Mountain View,
Calif.).
QTL experimental design
Quantitative trait (QTL) analysis was examined with attention to
experimental design and analysis. Dave Webb, Pioneer Hi-Bred,
Johnston, Iowa, looked at soybean cyst-nematode resistance; one
soybean introduction was found to have more resistance than any
other soybean tested to date. Three resistance loci were
identified; with this information the effect of population size
in detecting the traits was tested. Large sample populations
were found to be essential in finding and mapping these traits.
The minimum sample population size is 200.
The need for large sample populations was again emphasized by
Karl Lark, University of Utah, Salt Lake City. Lark found that
specialized statistical methods and graphing were needed to
identify many important loci. Specifically, Lark identified
interacting traits a condition called epistasis. One trait
measured on its own had no effect on plant height. This same
trait was found to interact with another plant height QTL and
could explain 25% of the plant height variation. The basis of
Lark's technique is to use large population sizes and to conduct
pairwise comparisons of loci in plants with extreme phenotypes.
The results are graphed and epistatic interactions are then
identified. According to Thomas Cheesbrough, South Dakota State
University, Brookings, this type of analysis will be essential to
study the genes of such metabolic pathways as oil production,
because each enzyme is highly interdependent on the gene products
of the entire metabolic chain.
Mapping Technologies
Mapping technologies were featured in several talks and posters
throughout the conference. Perry Cregan, USDA, ARS, Beltsville,
Md., and others reported on the continued success with simple
sequence repeats (SSR). The SSR's are small sequence patterns
which are repeated at variable lengths. The variable length of
the repeats provides a means to identify varieties and
individuals; tools needed by crop breeders and geneticists. In
addition to SSR technology, amplified fragment length
polymorphism (AFLP), a related new technology, was reported by
Drs. Pieter Vos and Marc Zabeau, KeyGene, Wageningen, The
Netherlands. AFLP will provide markers for those map regions
which other markers have not successfully bridged. The AFLP
technique has the capacity to exploit multiple forms of variation
within the genome. The new technology described by Vos is still
a long way from direct application by plant breeders as discussed
at the International Triticale Mapping Initiative meeting held in
San Diego in conjunction with the Plant Genome II conference.
Plant Genome III
Plant Genome III will be held January 15-19, 1995, in San Diego,
Calif. Sessions will address all aspects of mapping, from QTL's
to the latest molecular marker technologies, instrumentation, and
gene isolation. For more information or program suggestions
contact: Jerome Miksche or Stephen Heller, USDA/ARS, BARC-W,
Bldg. 005, Room 331-C, Beltsville, MD 20705 USA.